Six years ago, 3D cinema seemed about as likely a candidate for a revival as Odorama. Today it owns the multiplex. After swiftly dominating CG animated features, it gained toe-holds in horror, action and concert films, achieving inarguable momentum even before the success of Avatar.

Now – objectionable as it might be to refuseniks such as Walter Murch, Roger Ebert or Mark Kermode – it is the default form for major studio franchises. From Transformers 3 to Pirates 4, Green Lantern to Thor, the Harry Potter climax to the Spider-Man reboot, almost any picture aiming to dominate the box office is now filmed stereoscopically.

Big deal, you might think. Popcorn fodder will always latch on to sensational fads. But something else is going on, too. Whether through passion or contingency, increasing numbers of serious directors with critical credibility are embracing 3D for their own ends.

Take Werner Herzog, not exactly a film-maker renowned for jumping on bandwagons or following the path of least resistance. "I've said in public that I'm a sceptic about 3D," he recently told me. "It will not take over everything. That's an illusion. Not every film in 20 years' time is going to be in 3D." But for certain projects, he now thinks, it's the only choice.

Next week sees the release of Cave of Forgotten Dreams, his documentary about the extraordinary paleolithic paintings at Chauvet in the south of France. 3D, Herzog felt, was the only technology able to convey the dramatic play between the images and the fluctuating surfaces on which they were painted. (It's also great for capturing claustrophobic spaces.) He followed this instinct to deploy an unfamiliar, work-intensive technology despite having very limited access to caves with little light or room to manoeuvre. The results are spectacular.

Next month brings another terrific documentary by an august German auteur who felt artistically compelled to use 3D (and, incidentally, in another film feted at Berlin). Pina is Wim Wenders's tribute to the late choreographer Pina Bausch. Like Herzog, he had to grapple with unfamiliar, often unwieldy equipment under highly constricted shooting circumstances as he tried to capture Bausch's company in action, close up. His aim, he has said, is not conspicuous spectacle but the sense that the audience is sharing the performance space: "The plasticity should not call attention to itself but should make itself almost invisible, so that Pina's art becomes even more evident."

This immersive approach to recording performance has already proven viable with pop acts (Miley Cyrus, Justin Bieber) and opera (the recently released Carmen 3D), but Wenders takes the use of stereo photography further to convey artists' movement through space. For him, the improved capacity of the latest equipment to record normal human movement, with far less of the strobing effect sometimes associated with 3D, opens up many opportunities. "I believe the future of this technology does not necessarily lie where it is being used at the moment, in fantasy films," he has said. See where the technology leads before dismissing it – "No one would have though that digital cinema would ultimately save and reinvent documentary film-making."

Other major directors seem to agree. Martin Scorsese is currently shooting his first 3D feature, the children's adventure Hugo Cabret, and has called the technology "liberating". "It's literally a Rubik's Cube every time you go out to design a shot," he told the Observer . Inadvertently echoing Wenders's experience, he said the effect of 3D on actors is "as if sculpture is moving in a way, like dancers".

Steven Soderbergh has also worked on two abortive 3D projects, Contagion (eventually shot in 2D instead) and a Cleopatra musical. "I want to see the first person take a shot at doing a straight drama in 3D," he has said. "Maybe the way to do it would be to make a period drama in 3D where it really contributes to your sense of being in that world. Cleopatra's world would be a natural for this."

Perhaps Baz Luhrmann thinks the same of the jazz age – that might explain his decision to use 3D for his adaptation of The Great Gatsby, a story heavier on conversation and decor than spectacle or action, though its party scenes must also appeal to the expressive director of Moulin Rouge.

Of course, plenty of other big-name directors are unashamedly embracing 3D's potential for fantasy spectacle. Special attention is being paid to the way it can combine with computer-generated environments navigable in three dimensions that would normally be unavailable to a film crew, such as aquatic or mid-air settings. Steven Spielberg's forthcoming motion-capture movie The Adventures of Tintin: Secret of the Unicorn, produced with Peter Jackson, is based on a story with ample scope for underwater exploration, as is David Fincher's first tentpole picture, Disney's 20,000 Leagues Under the Sea.

Guillermo del Toro's abandoned HP Lovecraft adaptation At the Mountains of Madness, meanwhile, was specifically conceived in 3D for what Del Toro described to the New Yorker as "the aquarium effect" – despite being set on land, in an Antarctic city built by fearsome aliens:

In motion, [Del Toro] explained, the [creatures] would appear buoyant — "unbound by gravity". As the camera tracked them roaming around the city, the viewer would feel disoriented, like a panicked scuba diver inside a cave. "We designed the creatures in such a way that they can go forward or backward, or hang, or be vertical, and they still make sense," he said.

Having colonised the multiplex, 3D has now taken the imaginations of Hollywood's most celebrated directors. As the technology grows cheaper and more accessible, a new generation of film-makers – not all of them, but many – will work in the format from the start. When they come of age, the scope of 3D's expressive potential will be revealed.